cls.AnnotationCorpus.CAnnotationCorpus Class Reference

Annotation corpus. More...

Inheritance diagram for cls.AnnotationCorpus.CAnnotationCorpus:

Collaboration diagram for cls.AnnotationCorpus.CAnnotationCorpus:

Public Member Functions
def	__init__ (s, name)
def	Add (s, goID, elemName)
	Add a ontology/entity relationship. More...
def	GetGOIDs (s)
	Get all ontology identifiers. More...
def	GetElementsByGOID (s, goID)
	Get all elements associated with a particular ontology term. More...
def	Merge (s, ac)
	Update this corpus with the contents of another corpus. More...
def	GetElementCount (s, goID)
	Get the number of elements associated with a particular ontology term. More...
def	GetGOIDsByElement (s, elemName)
	Get the ontology identifiers associated with an element. More...
def	GetElements (s)
	Get all entities associated with GO IDs. More...
def	Read (s, ffn)
	Read a simplified annotation corpus data file. More...
def	Write (s, ffn)
	Store annotation corpus to a file. More...

Detailed Description

Annotation corpus.

This class holds both mappings from GO IDs to associated entities
(eg. proteins) and vice versa. For large corpora, this can be very memory
demanding!

Constructor & Destructor Documentation

__init__()

def cls.AnnotationCorpus.CAnnotationCorpus.__init__	(		s,
			name
	)

     @param name Namespace name, eg. 'biological_process'.

Member Function Documentation

Add()

def cls.AnnotationCorpus.CAnnotationCorpus.Add	(		s,
			goID,
			elemName
	)

Add a ontology/entity relationship.

    @param goID  Ontology identifier, usually the GO ID.
    @param elemName  Element name the ontology identifier is associated
     with, usually a protein accession number.

GetElementCount()

def cls.AnnotationCorpus.CAnnotationCorpus.GetElementCount	(		s,
			goID
	)

Get the number of elements associated with a particular ontology term.

Parameters

goID	Ontology identifier, usually the GO ID.

Returns

(int) Can be zero if goID has not been associated with any element.

GetElements()

def cls.AnnotationCorpus.CAnnotationCorpus.GetElements

(

s

)

Get all entities associated with GO IDs.

    Report all elements that have been associated with a GO ID.
    @return @c List of @c strings.

GetElementsByGOID()

def cls.AnnotationCorpus.CAnnotationCorpus.GetElementsByGOID	(		s,
			goID
	)

Get all elements associated with a particular ontology term.

    @param goID  Ontology identifier, usually the GO ID.
    @return A list of element names (@c strings). Can be empty if @c goID
    has not been associated with any element.

GetGOIDs()

def cls.AnnotationCorpus.CAnnotationCorpus.GetGOIDs

(

s

)

Get all ontology identifiers.

    Report all GO identifiers that have been associated with an element.
    @return @c List of @c strings.

GetGOIDsByElement()

def cls.AnnotationCorpus.CAnnotationCorpus.GetGOIDsByElement	(		s,
			elemName
	)

Get the ontology identifiers associated with an element.

    @param elemName  Element name the ontology identifier to be queried,
    usually a protein accession number.
    @return @c List of GO IDs (@c strings).

Merge()

def cls.AnnotationCorpus.CAnnotationCorpus.Merge	(		s,
			ac
	)

Update this corpus with the contents of another corpus.

    @param ac  A @ref CAnnotationCorpus object.

Read()

def cls.AnnotationCorpus.CAnnotationCorpus.Read	(		s,
			ffn
	)

Read a simplified annotation corpus data file.

    Reads ontology/entity relationships previously dumped by the @ref
    Write method of this object. Does not read GAF files.
    @param ffn  Full path file name, must be writable.

Write()

def cls.AnnotationCorpus.CAnnotationCorpus.Write	(		s,
			ffn
	)

Store annotation corpus to a file.

    Dumps a tab-separated file for quick reading of this annotation
    corpus. This should not be confused with cls.GAFReader.CGAFReader, as
    this method here stores only ontology/entity relationships deposited
    in this object without any additional information as would be done for
    GAF files.
    @param ffn  Full path file name, must be writable.

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The documentation for this class was generated from the following file:

• cls/AnnotationCorpus.py